Genomic analysis of ICEVchBan8: An atypical genetic element in Vibrio cholerae

Abstract

Genomic islands (GIs) and integrative conjugative elements (ICEs) are major players in bacterial evolution since they encode genes involved in adaptive functions of medical or environmental importance. Here we performed the genomic analysis of ICEVchBan8, an unusual ICE found in the genome of a clinical non-toxigenic Vibrio cholerae O37 isolate. ICEVchBan8 shares most of its genetic structure with SXT/R391 ICEs. However, this ICE codes for a different integration/excision module is located at a different insertion site, and part of its genetic cargo shows homology to other pathogenicity islands of V. cholerae.

Fig. 1

Structural comparison between SXT and ICEVchBan8. A genetic map of core genes shared between the two ICEs (light gray) is shown. Specific regions for SXT and ICEVchBan8 are depicted in blue and red, respectively. Dark gray indicates inverted genes setR/eex. Hotspot insertions are indicated by dotted arrows, as shown in the above (SXT) and below (ICEVchBan8) the shared backbone.

Fig. 2

Muscle alignment of the predicted amino acid sequences of: (a) xis_BAN8, VefA of VPI-2 from V. cholerae N16961 and putative RDF of MGIVchUSA1 from V. cholerae RC385 and (b) SetR of ICEVchBan8, SetR of SXT from V. cholerae MO10 and SetR of ICEVchInd5 from V. cholerae 7452. The first 145aa of SetR are identical in all the three sequences. Amino acids conserved in all sequences are shown in red; amino acids conserved in two of three sequences are shown in pink. Gaps and amino acids divergent in all three sequences are shown in blue. Consensus sequence is depicted below the alignment.

Fig. 3

Hypothetical model of ICEVchBan8 formation. (1) A fragment of an unknown mobile genetic element (shown in red) transposes into the variable region IV (VR IV) of the SXT/R391 precursor of ICEVchBan8 (shown in blue), with the same mechanism responsible for acquisition of the new genetic material in the hotspots. (2a or 2b) During transposition or in an unknown subsequent event, the 3′ region of ICEVchBan8 precursor undergoes inversion rearrangement. This inversion causes loss of the old attR site, triggering excision of the rearranged element from the prfC locus. (3) During abnormal excision, the ICE loses the 5′ region containing the original integration module (int_SXT). This event may also result from competition between two integration modules in the linear or circular form. (4) Reintegration of the newborn ICEVchBan8 in VPI-2 locus is catalyzed by the new integrase (int_Ban8).